From eda8ca9e4823bbc462181a4c25cb2161d9fb7924 Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Tue, 7 Jul 2026 16:19:29 -0400
Subject: [PATCH 01/12] feat (closes #7246): add new component:
 leafcutter/differentialsplicing

---
 .../differentialsplicing/environment.yml      |   7 +
 .../leafcutter/differentialsplicing/main.nf   |  42 ++++++
 .../leafcutter/differentialsplicing/meta.yml  |  80 ++++++++++++
 .../differentialsplicing/tests/main.nf.test   | 121 ++++++++++++++++++
 .../tests/main.nf.test.snap                   |  93 ++++++++++++++
 .../tests/nextflow.config                     |   7 +
 6 files changed, 350 insertions(+)
 create mode 100644 modules/nf-core/leafcutter/differentialsplicing/environment.yml
 create mode 100644 modules/nf-core/leafcutter/differentialsplicing/main.nf
 create mode 100644 modules/nf-core/leafcutter/differentialsplicing/meta.yml
 create mode 100644 modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
 create mode 100644 modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config

diff --git a/modules/nf-core/leafcutter/differentialsplicing/environment.yml b/modules/nf-core/leafcutter/differentialsplicing/environment.yml
new file mode 100644
index 000000000000..e4c971910da0
--- /dev/null
+++ b/modules/nf-core/leafcutter/differentialsplicing/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::leafcutter=2.0.3"
diff --git a/modules/nf-core/leafcutter/differentialsplicing/main.nf b/modules/nf-core/leafcutter/differentialsplicing/main.nf
new file mode 100644
index 000000000000..7e2279bc76fc
--- /dev/null
+++ b/modules/nf-core/leafcutter/differentialsplicing/main.nf
@@ -0,0 +1,42 @@
+process LEAFCUTTER_DIFFERENTIALSPLICING {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/leafcutter:2.0.3--pyhd8ed1ab_0':
+        'quay.io/biocontainers/leafcutter:2.0.3--pyhd8ed1ab_0' }"
+
+    input:
+    tuple val(meta), path(counts), path(groups)
+
+    output:
+    tuple val(meta), path("*_cluster_significance.txt"), emit: cluster_significance
+    tuple val(meta), path("*_effect_sizes.txt")        , emit: effect_sizes
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    tuple val("${task.process}"), val('leafcutter'), val("2.0.3"), topic: versions, emit: versions_leafcutter
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    export USER=\${USER:-nobody}
+
+    leafcutter-ds \\
+        $counts \\
+        $groups \\
+        --output_prefix ${prefix}_results \\
+        --num_threads $task.cpus \\
+        $args
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_results_cluster_significance.txt
+    touch ${prefix}_results_effect_sizes.txt
+    """
+}
diff --git a/modules/nf-core/leafcutter/differentialsplicing/meta.yml b/modules/nf-core/leafcutter/differentialsplicing/meta.yml
new file mode 100644
index 000000000000..cd5a48fb2bd9
--- /dev/null
+++ b/modules/nf-core/leafcutter/differentialsplicing/meta.yml
@@ -0,0 +1,80 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "leafcutter_differentialsplicing"
+description: Perform differential splicing analysis to identify junctions with significant changes in splicing between conditions
+keywords:
+  - alternative splicing
+  - differential splicing
+  - RNA-seq
+  - intron usage
+tools:
+  - "leafcutter":
+      description: "Annotation-free quantification of RNA splicing from RNA-seq data"
+      homepage: "https://leafcutter2.github.io/leafcutter-ds/"
+      documentation: "https://leafcutter2.github.io/leafcutter-ds/tutorials/differential-splicing/"
+      tool_dev_url: "https://github.com/leafcutter2/leafcutter-ds"
+      doi: "10.1038/s41588-017-0004-9"
+      licence: ["Apache-2.0"]
+      identifier: biotools:leafcutter
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test' ]`
+    - counts:
+        type: file
+        description: Intron usage counts file from leafcutter-cluster (either perind.counts.gz or perind_numers.counts.gz)
+        pattern: "*.counts.gz"
+    - groups:
+        type: file
+        description: Tab-delimited file with sample names in column 1 and sample group/phenotype assignments in column 2
+        pattern: "*.txt"
+
+output:
+  cluster_significance:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*_cluster_significance.txt":
+          type: file
+          description: Cluster-level differential splicing statistics including p-values and test status
+          pattern: "*_cluster_significance.txt"
+  effect_sizes:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*_effect_sizes.txt":
+          type: file
+          description: Per-intron junction effect sizes, PSI values, and delta PSI for each condition
+          pattern: "*_effect_sizes.txt"
+  versions_leafcutter:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "leafcutter":
+          type: string
+          description: The name of the tool
+      - "2.0.3":
+          type: string
+          description: The version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - leafcutter:
+          type: string
+          description: The name of the tool
+      - "2.0.3":
+          type: string
+          description: The version of the tool
+authors:
+  - "@JTL-lab"
+maintainers:
+  - "@JTL-lab"
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
new file mode 100644
index 000000000000..a0625cd168e4
--- /dev/null
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
@@ -0,0 +1,121 @@
+nextflow_process {
+
+    name "Test Process LEAFCUTTER_DIFFERENTIALSPLICING"
+    script "../main.nf"
+    process "LEAFCUTTER_DIFFERENTIALSPLICING"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "leafcutter"
+    tag "leafcutter/differentialsplicing"
+    tag "leafcutter/clusterregtools"
+    tag "regtools"
+    tag "regtools/junctionsextract"
+
+    test("homo_sapiens - bam - differential splicing") {
+
+        config "./nextflow.config"
+
+        setup {
+            run("REGTOOLS_JUNCTIONSEXTRACT") {
+                script "../../../regtools/junctionsextract/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of(
+                        [
+                            [ id:'ctrl_rep1', single_end:false ],
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                        ],
+                        [
+                            [ id:'ctrl_rep2', single_end:false ],
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                        ],
+                        [
+                            [ id:'kd_rep1', single_end:false ],
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                        ],
+                        [
+                            [ id:'kd_rep2', single_end:false ],
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                        ]
+                    )
+                    input[1] = ''
+                    """
+                }
+            }
+
+            run("LEAFCUTTER_CLUSTERREGTOOLS") {
+                script "../../../leafcutter/clusterregtools/main.nf"
+                process {
+                    """
+                    input[0] = REGTOOLS_JUNCTIONSEXTRACT.out.junc
+                        .map { meta, junc -> junc }
+                        .collect()
+                        .map { junc_files -> [ [ id:'test_ds' ], junc_files ] }
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                def groups_content = '''ctrl_rep1\\tCONTROL
+ctrl_rep2\\tCONTROL
+kd_rep1\\tKNOCKDOWN
+kd_rep2\\tKNOCKDOWN
+'''
+                def groups_file = file("\${workDir}/groups_file.txt")
+                groups_file.text = groups_content
+
+                input[0] = LEAFCUTTER_CLUSTERREGTOOLS.out.numers
+                    .map { meta, counts -> [ meta, counts, groups_file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.cluster_significance,
+                    process.out.effect_sizes,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bam - differential splicing - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file('test_perind.counts.gz'),
+                    file('groups_file.txt')
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.cluster_significance != null },
+                { assert process.out.effect_sizes != null }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
new file mode 100644
index 000000000000..bf1193bdcd1e
--- /dev/null
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
@@ -0,0 +1,93 @@
+{
+    "homo_sapiens - bam - differential splicing": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test_ds"
+                    },
+                    "test_ds_results_cluster_significance.txt:md5,222cfb8c25277ec24f84934b684d195a"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test_ds"
+                    },
+                    "test_ds_results_effect_sizes.txt:md5,8535426635beacabae83a5b8cc6ed385"
+                ]
+            ],
+            {
+                "versions_leafcutter": [
+                    [
+                        "LEAFCUTTER_DIFFERENTIALSPLICING",
+                        "leafcutter",
+                        "2.0.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-07T15:56:29.391725645",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.0"
+        }
+    },
+    "homo_sapiens - bam - differential splicing - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_results_cluster_significance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_results_effect_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        "LEAFCUTTER_DIFFERENTIALSPLICING",
+                        "leafcutter",
+                        "2.0.3"
+                    ]
+                ],
+                "cluster_significance": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_results_cluster_significance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "effect_sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_results_effect_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_leafcutter": [
+                    [
+                        "LEAFCUTTER_DIFFERENTIALSPLICING",
+                        "leafcutter",
+                        "2.0.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-07T15:56:35.602866997",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.0"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
new file mode 100644
index 000000000000..b859f0a57a23
--- /dev/null
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: 'LEAFCUTTER_DIFFERENTIALSPLICING' {
+        ext.args = '--min_samples_per_group 2 --min_samples_per_intron 2 --num_threads 1'
+    }
+
+}

From 58b53d42168b0db24d4ad7fd9ed82685da40104c Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Wed, 8 Jul 2026 14:49:27 -0400
Subject: [PATCH 02/12] fix: update main.nf.test for non-deterministic outputs,
 update snapshot, set python environment hash variable

---
 .../leafcutter/differentialsplicing/main.nf   |  2 ++
 .../differentialsplicing/tests/main.nf.test   | 11 +++++---
 .../tests/main.nf.test.snap                   | 28 ++++++-------------
 3 files changed, 18 insertions(+), 23 deletions(-)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/main.nf b/modules/nf-core/leafcutter/differentialsplicing/main.nf
index 7e2279bc76fc..af77288e2ab7 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/main.nf
+++ b/modules/nf-core/leafcutter/differentialsplicing/main.nf
@@ -24,6 +24,8 @@ process LEAFCUTTER_DIFFERENTIALSPLICING {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     export USER=\${USER:-nobody}
+    export PYTHONHASHSEED=0
+    export CUBLAS_WORKSPACE_CONFIG=:4096:8
 
     leafcutter-ds \\
         $counts \\
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
index a0625cd168e4..e65c5a4c5a69 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
@@ -82,10 +82,13 @@ kd_rep2\\tKNOCKDOWN
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.cluster_significance,
-                    process.out.effect_sizes,
-                    process.out.findAll { key, val -> key.startsWith('versions') }
-                ).match() }
+                    process.out.findAll { key, val -> key.startsWith('versions') },
+                    process.out.cluster_significance.collect { file(it[1]).getName() },
+                    process.out.effect_sizes.collect { file(it[1]).getName() }
+                ).match() },
+                // Check non-deterministic files exist
+                { assert file(process.out.cluster_significance[0][1]).exists() },
+                { assert file(process.out.effect_sizes[0][1]).exists() }
             )
         }
 
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
index bf1193bdcd1e..35c2e90c45dd 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
@@ -1,22 +1,6 @@
 {
     "homo_sapiens - bam - differential splicing": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test_ds"
-                    },
-                    "test_ds_results_cluster_significance.txt:md5,222cfb8c25277ec24f84934b684d195a"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test_ds"
-                    },
-                    "test_ds_results_effect_sizes.txt:md5,8535426635beacabae83a5b8cc6ed385"
-                ]
-            ],
             {
                 "versions_leafcutter": [
                     [
@@ -25,9 +9,15 @@
                         "2.0.3"
                     ]
                 ]
-            }
+            },
+            [
+                "test_ds_results_cluster_significance.txt"
+            ],
+            [
+                "test_ds_results_effect_sizes.txt"
+            ]
         ],
-        "timestamp": "2026-07-07T15:56:29.391725645",
+        "timestamp": "2026-07-08T14:38:48.580335473",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
@@ -84,7 +74,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-07T15:56:35.602866997",
+        "timestamp": "2026-07-08T14:39:52.087856717",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"

From e80e3b3e932a478fc6cc6acd626309e9cccc8dcd Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Tue, 28 Jul 2026 14:36:45 -0400
Subject: [PATCH 03/12] refactor, fix: incorporated cleaner syntax with
 sanitizeOutput for tests, removed redundant --num_threads param in test
 config args, move container options set in main.nf to main.nf.test and add
 note in meta.yml

---
 .../leafcutter/differentialsplicing/main.nf   |  4 --
 .../leafcutter/differentialsplicing/meta.yml  |  2 +
 .../differentialsplicing/tests/main.nf.test   | 15 ++----
 .../tests/main.nf.test.snap                   | 51 +++++++------------
 .../tests/nextflow.config                     |  5 +-
 5 files changed, 28 insertions(+), 49 deletions(-)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/main.nf b/modules/nf-core/leafcutter/differentialsplicing/main.nf
index af77288e2ab7..1f4f4a73e46d 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/main.nf
+++ b/modules/nf-core/leafcutter/differentialsplicing/main.nf
@@ -23,10 +23,6 @@ process LEAFCUTTER_DIFFERENTIALSPLICING {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    export USER=\${USER:-nobody}
-    export PYTHONHASHSEED=0
-    export CUBLAS_WORKSPACE_CONFIG=:4096:8
-
     leafcutter-ds \\
         $counts \\
         $groups \\
diff --git a/modules/nf-core/leafcutter/differentialsplicing/meta.yml b/modules/nf-core/leafcutter/differentialsplicing/meta.yml
index cd5a48fb2bd9..76ce8e363893 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/meta.yml
+++ b/modules/nf-core/leafcutter/differentialsplicing/meta.yml
@@ -78,3 +78,5 @@ authors:
   - "@JTL-lab"
 maintainers:
   - "@JTL-lab"
+notes:
+  - This module uses PyTorch for statistical analysis. When running in containers, you may need to set environment variables in your pipeline configuration for reproducibility. For example, `containerOptions = '--env USER=nobody --env PYTHONHASHSEED=0 --env CUBLAS_WORKSPACE_CONFIG=:4096:8'` (Docker) or `containerOptions = '--env USER=nobody,PYTHONHASHSEED=0,CUBLAS_WORKSPACE_CONFIG=:4096:8'` (Singularity/Apptainer).
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
index e65c5a4c5a69..a3a60ef74eb6 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
@@ -81,14 +81,7 @@ kd_rep2\\tKNOCKDOWN
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.findAll { key, val -> key.startsWith('versions') },
-                    process.out.cluster_significance.collect { file(it[1]).getName() },
-                    process.out.effect_sizes.collect { file(it[1]).getName() }
-                ).match() },
-                // Check non-deterministic files exist
-                { assert file(process.out.cluster_significance[0][1]).exists() },
-                { assert file(process.out.effect_sizes[0][1]).exists() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["cluster_significance", "effect_sizes"])).match()}
             )
         }
 
@@ -111,11 +104,9 @@ kd_rep2\\tKNOCKDOWN
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert process.out.cluster_significance != null },
-                { assert process.out.effect_sizes != null }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
index 35c2e90c45dd..8e5ecd5f5bc3 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
@@ -2,6 +2,22 @@
     "homo_sapiens - bam - differential splicing": {
         "content": [
             {
+                "cluster_significance": [
+                    [
+                        {
+                            "id": "test_ds"
+                        },
+                        "test_ds_results_cluster_significance.txt"
+                    ]
+                ],
+                "effect_sizes": [
+                    [
+                        {
+                            "id": "test_ds"
+                        },
+                        "test_ds_results_effect_sizes.txt"
+                    ]
+                ],
                 "versions_leafcutter": [
                     [
                         "LEAFCUTTER_DIFFERENTIALSPLICING",
@@ -9,15 +25,9 @@
                         "2.0.3"
                     ]
                 ]
-            },
-            [
-                "test_ds_results_cluster_significance.txt"
-            ],
-            [
-                "test_ds_results_effect_sizes.txt"
-            ]
+            }
         ],
-        "timestamp": "2026-07-08T14:38:48.580335473",
+        "timestamp": "2026-07-28T12:22:48.849459725",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
@@ -26,29 +36,6 @@
     "homo_sapiens - bam - differential splicing - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_results_cluster_significance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_results_effect_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        "LEAFCUTTER_DIFFERENTIALSPLICING",
-                        "leafcutter",
-                        "2.0.3"
-                    ]
-                ],
                 "cluster_significance": [
                     [
                         {
@@ -74,7 +61,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-08T14:39:52.087856717",
+        "timestamp": "2026-07-28T12:00:56.961347309",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
index b859f0a57a23..8fcb07502f79 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
@@ -1,7 +1,10 @@
 process {
 
     withName: 'LEAFCUTTER_DIFFERENTIALSPLICING' {
-        ext.args = '--min_samples_per_group 2 --min_samples_per_intron 2 --num_threads 1'
+        ext.args = '--min_samples_per_group 2 --min_samples_per_intron 2'
+        containerOptions = { workflow.containerEngine == 'singularity' ?
+            '--env USER=nobody,PYTHONHASHSEED=0,CUBLAS_WORKSPACE_CONFIG=:4096:8' :
+            '--env USER=nobody --env PYTHONHASHSEED=0 --env CUBLAS_WORKSPACE_CONFIG=:4096:8' }
     }
 
 }

From d17cd67fffeb844b3752add78d2bb819c5f00d8c Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Tue, 28 Jul 2026 23:56:13 -0400
Subject: [PATCH 04/12] fix: increase pullTimeout for singularity in test
 profile

---
 .../leafcutter/differentialsplicing/tests/nextflow.config   | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
index 8fcb07502f79..966a3f07d3a7 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
@@ -1,3 +1,7 @@
+singularity {
+    pullTimeout = 30.m
+}
+
 process {
 
     withName: 'LEAFCUTTER_DIFFERENTIALSPLICING' {
@@ -7,4 +11,4 @@ process {
             '--env USER=nobody --env PYTHONHASHSEED=0 --env CUBLAS_WORKSPACE_CONFIG=:4096:8' }
     }
 
-}
+}
\ No newline at end of file

From b28f3a720416fe3f275a5adffd6bd72e6986d071 Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Wed, 29 Jul 2026 00:06:14 -0400
Subject: [PATCH 05/12] refactor: add EOF space to nextflow.config for test
 profile

---
 .../leafcutter/differentialsplicing/tests/nextflow.config       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
index 966a3f07d3a7..9949e3230640 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
@@ -11,4 +11,4 @@ process {
             '--env USER=nobody --env PYTHONHASHSEED=0 --env CUBLAS_WORKSPACE_CONFIG=:4096:8' }
     }
 
-}
\ No newline at end of file
+}

From 833380495b697350b775a2f9e236546a9f320170 Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Thu, 30 Jul 2026 11:23:53 -0400
Subject: [PATCH 06/12] refactor: move environment variables from test config
 to module main.nf for better transparency as recommended, update meta.yml
 with note on what is set and why

---
 modules/nf-core/leafcutter/differentialsplicing/main.nf        | 3 +++
 modules/nf-core/leafcutter/differentialsplicing/meta.yml       | 2 +-
 .../leafcutter/differentialsplicing/tests/nextflow.config      | 3 ---
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/main.nf b/modules/nf-core/leafcutter/differentialsplicing/main.nf
index 1f4f4a73e46d..c5f90279cbc4 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/main.nf
+++ b/modules/nf-core/leafcutter/differentialsplicing/main.nf
@@ -23,6 +23,9 @@ process LEAFCUTTER_DIFFERENTIALSPLICING {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    export USER="\${USER:-nobody}"
+    export PYTHONHASHSEED=0
+
     leafcutter-ds \\
         $counts \\
         $groups \\
diff --git a/modules/nf-core/leafcutter/differentialsplicing/meta.yml b/modules/nf-core/leafcutter/differentialsplicing/meta.yml
index 76ce8e363893..570c7b7b40be 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/meta.yml
+++ b/modules/nf-core/leafcutter/differentialsplicing/meta.yml
@@ -79,4 +79,4 @@ authors:
 maintainers:
   - "@JTL-lab"
 notes:
-  - This module uses PyTorch for statistical analysis. When running in containers, you may need to set environment variables in your pipeline configuration for reproducibility. For example, `containerOptions = '--env USER=nobody --env PYTHONHASHSEED=0 --env CUBLAS_WORKSPACE_CONFIG=:4096:8'` (Docker) or `containerOptions = '--env USER=nobody,PYTHONHASHSEED=0,CUBLAS_WORKSPACE_CONFIG=:4096:8'` (Singularity/Apptainer).
+  - This module uses PyTorch for statistical analysis. Environment variables are automatically set in the module for container compatibility (`USER` defaults to 'nobody' if unset to prevent Pytorch cache initialization errors, `PYTHONHASHSEED=0` is set for reproducibility).
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
index 9949e3230640..289576488ca3 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
@@ -6,9 +6,6 @@ process {
 
     withName: 'LEAFCUTTER_DIFFERENTIALSPLICING' {
         ext.args = '--min_samples_per_group 2 --min_samples_per_intron 2'
-        containerOptions = { workflow.containerEngine == 'singularity' ?
-            '--env USER=nobody,PYTHONHASHSEED=0,CUBLAS_WORKSPACE_CONFIG=:4096:8' :
-            '--env USER=nobody --env PYTHONHASHSEED=0 --env CUBLAS_WORKSPACE_CONFIG=:4096:8' }
     }
 
 }

From b4a79454686b2e2eba73e1cd93ed186d763e67a3 Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Sat, 1 Aug 2026 13:25:15 -0400
Subject: [PATCH 07/12] docs: update tools section of meta.yml with args_id per
 nf-core docs best practices

---
 modules/nf-core/leafcutter/differentialsplicing/meta.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/meta.yml b/modules/nf-core/leafcutter/differentialsplicing/meta.yml
index 570c7b7b40be..e9f4624dc048 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/meta.yml
+++ b/modules/nf-core/leafcutter/differentialsplicing/meta.yml
@@ -15,6 +15,7 @@ tools:
       doi: "10.1038/s41588-017-0004-9"
       licence: ["Apache-2.0"]
       identifier: biotools:leafcutter
+      args_id: "$args"
 
 input:
   - - meta:

From b048a4f6ddf06b2008e688f4ccd3b16e8ad3b1fe Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Sat, 1 Aug 2026 13:33:29 -0400
Subject: [PATCH 08/12] refactor: move ext.args from nextflow.config to be with
 test input in main.nf.test per nf-core docs best practices

---
 .../leafcutter/differentialsplicing/tests/main.nf.test    | 8 ++++++++
 .../leafcutter/differentialsplicing/tests/nextflow.config | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
index a3a60ef74eb6..c756d7c5943d 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
@@ -62,6 +62,9 @@ nextflow_process {
         }
 
         when {
+            params {
+                module_args = '--min_samples_per_group 2 --min_samples_per_intron 2'
+            }
             process {
                 """
                 def groups_content = '''ctrl_rep1\\tCONTROL
@@ -89,9 +92,14 @@ kd_rep2\\tKNOCKDOWN
 
     test("homo_sapiens - bam - differential splicing - stub") {
 
+        config "./nextflow.config"
+
         options "-stub"
 
         when {
+            params {
+                module_args = ''
+            }
             process {
                 """
                 input[0] = [
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
index 289576488ca3..33a320a2dd72 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config
@@ -5,7 +5,7 @@ singularity {
 process {
 
     withName: 'LEAFCUTTER_DIFFERENTIALSPLICING' {
-        ext.args = '--min_samples_per_group 2 --min_samples_per_intron 2'
+        ext.args = { params.module_args ?: '' }
     }
 
 }

From bea36d8bec2c3b0ac1689fce80d78d03adc6b5b9 Mon Sep 17 00:00:00 2001
From: Julia Lewandowski <68295300+JTL-lab@users.noreply.github.com>
Date: Sun, 2 Aug 2026 15:22:50 -0400
Subject: [PATCH 09/12] Update
 modules/nf-core/leafcutter/differentialsplicing/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/leafcutter/differentialsplicing/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/main.nf b/modules/nf-core/leafcutter/differentialsplicing/main.nf
index c5f90279cbc4..c7fd29696581 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/main.nf
+++ b/modules/nf-core/leafcutter/differentialsplicing/main.nf
@@ -29,7 +29,7 @@ process LEAFCUTTER_DIFFERENTIALSPLICING {
     leafcutter-ds \\
         $counts \\
         $groups \\
-        --output_prefix ${prefix}_results \\
+        --output_prefix ${prefix} \\
         --num_threads $task.cpus \\
         $args
     """

From f3a1fc8c1683cd79e4eda7a75b47b03a9a6b3597 Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Mon, 3 Aug 2026 11:28:20 -0400
Subject: [PATCH 10/12] refactor: correct stub profile output file naming and
 main.nf.test.snap expected file naming following refactor in previous commit
 #bea36d8

---
 modules/nf-core/leafcutter/differentialsplicing/main.nf   | 4 ++--
 .../differentialsplicing/tests/main.nf.test.snap          | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/main.nf b/modules/nf-core/leafcutter/differentialsplicing/main.nf
index c7fd29696581..7ceb35307bf6 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/main.nf
+++ b/modules/nf-core/leafcutter/differentialsplicing/main.nf
@@ -37,7 +37,7 @@ process LEAFCUTTER_DIFFERENTIALSPLICING {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}_results_cluster_significance.txt
-    touch ${prefix}_results_effect_sizes.txt
+    touch ${prefix}_cluster_significance.txt
+    touch ${prefix}_effect_sizes.txt
     """
 }
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
index 8e5ecd5f5bc3..cf124e435216 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test_ds"
                         },
-                        "test_ds_results_cluster_significance.txt"
+                        "test_ds_cluster_significance.txt"
                     ]
                 ],
                 "effect_sizes": [
@@ -15,7 +15,7 @@
                         {
                             "id": "test_ds"
                         },
-                        "test_ds_results_effect_sizes.txt"
+                        "test_ds_effect_sizes.txt"
                     ]
                 ],
                 "versions_leafcutter": [
@@ -41,7 +41,7 @@
                         {
                             "id": "test"
                         },
-                        "test_results_cluster_significance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_cluster_significance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "effect_sizes": [
@@ -49,7 +49,7 @@
                         {
                             "id": "test"
                         },
-                        "test_results_effect_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_effect_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions_leafcutter": [

From 4632bf2956782bf96b054c0b5f07ac43872a9577 Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Tue, 4 Aug 2026 11:29:18 -0400
Subject: [PATCH 11/12] fix: update leafcutter/differentialsplicing
 main.nf.test and test snapshot to reflect now deterministic output files

---
 .../leafcutter/differentialsplicing/tests/main.nf.test      | 2 +-
 .../leafcutter/differentialsplicing/tests/main.nf.test.snap | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
index c756d7c5943d..07afc21e41f2 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
@@ -84,7 +84,7 @@ kd_rep2\\tKNOCKDOWN
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["cluster_significance", "effect_sizes"])).match()}
+                { assert snapshot(sanitizeOutput(process.out)).match()}
             )
         }
 
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
index cf124e435216..57a83f39641a 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test_ds"
                         },
-                        "test_ds_cluster_significance.txt"
+                        "test_ds_cluster_significance.txt:md5,fced1b0b3c0417c4f0c51eb2300d3441"
                     ]
                 ],
                 "effect_sizes": [
@@ -15,7 +15,7 @@
                         {
                             "id": "test_ds"
                         },
-                        "test_ds_effect_sizes.txt"
+                        "test_ds_effect_sizes.txt:md5,b2ca0c61567b8a78db594ac12fac1d5e"
                     ]
                 ],
                 "versions_leafcutter": [
@@ -27,7 +27,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-28T12:22:48.849459725",
+        "timestamp": "2026-08-04T11:23:11.169540122",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"

From 0faf3b9d09bbebe24e556398a649bc20ee81445c Mon Sep 17 00:00:00 2001
From: = <juliatlewand@gmail.com>
Date: Tue, 4 Aug 2026 11:58:23 -0400
Subject: [PATCH 12/12] Revert "fix: update leafcutter/differentialsplicing
 main.nf.test and test snapshot to reflect now deterministic output files"

This reverts commit 4632bf2956782bf96b054c0b5f07ac43872a9577.
---
 .../leafcutter/differentialsplicing/tests/main.nf.test      | 2 +-
 .../leafcutter/differentialsplicing/tests/main.nf.test.snap | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
index 07afc21e41f2..c756d7c5943d 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test
@@ -84,7 +84,7 @@ kd_rep2\\tKNOCKDOWN
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out)).match()}
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["cluster_significance", "effect_sizes"])).match()}
             )
         }
 
diff --git a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
index 57a83f39641a..cf124e435216 100644
--- a/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
+++ b/modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test_ds"
                         },
-                        "test_ds_cluster_significance.txt:md5,fced1b0b3c0417c4f0c51eb2300d3441"
+                        "test_ds_cluster_significance.txt"
                     ]
                 ],
                 "effect_sizes": [
@@ -15,7 +15,7 @@
                         {
                             "id": "test_ds"
                         },
-                        "test_ds_effect_sizes.txt:md5,b2ca0c61567b8a78db594ac12fac1d5e"
+                        "test_ds_effect_sizes.txt"
                     ]
                 ],
                 "versions_leafcutter": [
@@ -27,7 +27,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-08-04T11:23:11.169540122",
+        "timestamp": "2026-07-28T12:22:48.849459725",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"